Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.
Abstract
BACKGROUND: In recent years large bibliographic databases have made much of the published
literature of biology available for searches. However, the capabilities of the search
engines integrated into these databases for text-based bibliographic searches are
limited. To enable searches that deliver the results expected by comparative anatomists,
an underlying logical structure known as an ontology is required. DEVELOPMENT AND
TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO),
a multi-species ontology focused on anatomical structures that participate in feeding
and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple,
computable, definition of each muscle, which includes its attachments and innervation,
is true across mammals. This construction mirrors the logical foundation of comparative
anatomy and permits searches using language familiar to biologists. Further, it provides
a template for muscles that will be useful in extending any anatomy ontology. The
MFMO is developed to support the Feeding Experiments End-User Database Project (FEED,
https://feedexp.org/), a publicly-available, online repository for physiological data
collected from in vivo studies of feeding (e.g., mastication, biting, swallowing)
in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific
implementations of Textpresso, a text-mining system that facilitates powerful searches
of a corpus of scientific publications. We evaluate the MFMO by asking questions that
test the ability of the ontology to return appropriate answers (competency questions).
We compare the results of queries of the MFMO to results from similar searches in
PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the
MFMO is competent to answer queries formed in the common language of comparative anatomy,
but PubMed and Google Scholar are not. Overall, our results show that by incorporating
anatomical ontologies into searches, an expanded and anatomically comprehensive set
of results can be obtained. The broader scientific and publishing communities should
consider taking up the challenge of semantically enabled search capabilities.
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https://hdl.handle.net/10161/11696Published Version (Please cite this version)
10.1371/journal.pone.0149102Publication Info
Druzinsky, Robert E; Balhoff, James P; Crompton, Alfred W; Done, James; German, Rebecca
Z; Haendel, Melissa A; ... Wall, Christine E (2016). Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of
the Literature on the Feeding Muscles of Mammals. PLoS One, 11(2). pp. e0149102. 10.1371/journal.pone.0149102. Retrieved from https://hdl.handle.net/10161/11696.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Hilmar Lapp
Dir, IT
Christine Elizabeth Wall
Research Professor Emerita of Evolutionary Anthropology
The focus of my work is the functional and evolutionary anatomy of the head, with
an emphasis on how the feeding apparatus works and how it influences and is influenced
by other structures and functions. My research focuses primarily on the functional
anatomy of extant and extinct primates, but I am also interested in other mammalian
groups.
Current research projects include:
(1) a detailed study of the architecture, fiber types, and the recruitment patterns
of the jaw adductor muscl
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